Does the location of the signature take place at the spell casters location OR where the spell took affect (target).
Both (unless perhaps if it explicitly changed since 5th edition).
Mage Flamestrikes a person, but the person gets away. Does the signature stay with the person, like barrel rifling on a bullet?
The signature of the Flamestrike spell will linger at the location from where the magician cast the spell as well as on the subject of the spell.
The signature of a Fireball spell will linger at the location from where the magician cast the spell as well as at the location where the spell had effect.
Does the cleaning/astral signature work on sustained spells ie "Increased Reflexes"?
Active magic (like an active spell, a sustained spell, a permanent spell that have not yet turned permanent, a projecting magician, a preparation, a spirit, a medicine lodge etc etc) will always have the signature of the responsible magician, this can not be scrubbed away.
You can use it to scrub off the lingering signature from the location where the magician originally cast the spell. It can also be used on the signature that will linger on the subject once the spell is no longer sustained.
Is the signature where you cast the spell, or does it follow the mage around.
You will leave your signature where you cast the spell. If you drive by cast a spell from inside a van you will leave your signature inside the van. If you cast a spell in an office cubicle then you will leave the signature in that office cubicle.
You will also leave the signature at the target of the spell. If you cast a spell on a subject then your signature will linger will on the subject. If you cast a spell on a location then your signature will linger at that object.